Happy new year! Since February 2014, some FightAIDS@Home experiments have been using
AutoDock Flexible Vina.
Note: one AutoDock "batch" involves docking up to 1,000 compounds, while one AD Vina batch involves docking up to 10,000 compounds.
Batches of Vina Experiments starting from Experiment 149 (from batch 865236) now include up to 100K compounds.

Experiments 143 to 148 (AutoDock), 0% completed

Experiments 143 through 148 target the LEDGF site of HIV integrase. These experiments involve screening 6 libraries (Full NCI,
Enamine, ChemBridge, Asinex,
Vitas-M and Maybridge). These experiments will help distinguish better
sites of among a group of receptor structures even within the same structure. To help read structures in the table below, the "a" and "b" after the 4-character PDB ID designate
those receptor structures with alternate residue positions, while the "a" and "b" with the sites (FBP, LEDGF, Y3) designate different sites for the same symmetric structure of HIV IN.

TARGET: LEDGFb Site of HIV Integrase

AD Exp. 143

AD Exp. 144

AD Exp. 145

AD Exp. 146

AD Exp. 147

AD Exp. 148

Receptor Structure

Full NCI

Enamine

ChemBridge

Asinex

Vitas-M

Maybridge

PDB 4GVMa, LEDGF Site 2

824077-824393

825345-827689

834725-835738

838781-839287

840809-842312

846825-846901

PDB 4GVMb, LEDGF Site 2

824394-824710

827690-830034

835739-836752

839288-839794

842313-843816

846902-846978

PDB 4GW6a, LEDGF Site 2

824711-825027

830035-832379

836753-837766

839795-840301

843817-845320

846979-847055

PDB 4GW6b, LEDGF Site 2

825028-825344

832380-834724

837767-838780

840302-840808

845321-846824

847056-847132

COMPLETION

0%

0%

0%

0%

0%

0%

Experiments 139 to 142 (AD and AD Vina), 12% completed

Experiments 139 through 142 are two studies that each target the the combined receptors thus far used for AutoDock Vina. For each study, AutoDock and AD Vina screen either the NCI Diversity Set II* or the Full NCI Set; hence, there are 4 main groupings of virtual screenings. Experiments 139 and 140 will explore the calibration of a receptor when multiple receptors are involved in a virtual screening. Experiments 141 and 142 will investigate the effect of re-orienting the grid box by systematically rotating and translating a protein structure. In these cases, the LEDGF site of the HIV-1 integrase receptor from PDB 3NF8 is used, 1800 versions.
*Note: the current version of the NCI Diversity Set is IV.

TARGET: All Sites of AD Vina Receptors Thus Far

AD Exp. 139AutoDock

AD Exp. 140AD Vina

Receptor Structure

NCI Div. 2

NCI Div. 2

Current Vina Receptors

761260-765337

762338-762876

COMPLETION

24%

0%

TARGET: Rotated/Translated PDB 3NF8, LEDGF Site

AD Exp. 141AutoDock

AD Exp. 142AD Vina

Receptor Structure

NCI Div. 2

Full NCI

Rotated/Translated PDB 3NF8 (x1800)

762877-764676

764677-824076

COMPLETION

22%

0%

Experiments 133 to 138 (AD Vina), 45% completed

Experiments 133 through 138 target the dimer cavity (between the 2 LEDGF sites) of HIV integrase. These experiments involve screening 6 libraries (Full NCI,
Enamine, ChemBridge, Asinex,
Vitas-M and Maybridge). These experiments will help determine the differences
and utility of varying the dimensions of a "docking box."

TARGET: dimer cavity site of IN

AD Exp. 133AD Vina Exp. 79

AD Exp. 134AD Vina Exp. 80

AD Exp. 135AD Vina Exp. 81

AD Exp. 136AD Vina Exp. 82

AD Exp. 137AD Vina Exp. 83

AD Exp. 138AD Vina Exp. 84

Receptor Structure

Full NCI

Enamine

ChemBridge

Asinex

Vitas-M

Maybridge

PDB 3AO1, dimer cavity

732310-732341

733910-734144

745660-745761

750760-750810

753310-753460

760860-760867

PDB 3AO2, dimer cavity

732342-732373

734145-734379

745762-745863

750811-750861

753461-753611

760868-760875

PDB 3AV9a, dimer cavity

732374-732405

734380-734614

745864-745965

750862-750912

753612-753762

760876-760883

PDB 3AV9b, dimer cavity

732406-732437

734615-734849

745966-746067

750913-750963

753763-753913

760884-760891

PDB 3AVAa, dimer cavity

732438-732469

734850-735084

746068-746169

750964-751014

753914-754064

760892-760899

PDB 3AVAb, dimer cavity

732470-732501

735085-735319

746170-746271

751015-751065

754065-754215

760900-760907

PDB 3AVCa, dimer cavity

732502-732533

735320-735554

746272-746373

751066-751116

754216-754366

760908-760915

PDB 3AVCb, dimer cavity

732534-732565

735555-735789

746374-746475

751117-751167

754367-754517

760916-760923

PDB 3AVFa, dimer cavity

732566-732597

735790-736024

746476-746577

751168-751218

754518-754668

760924-760931

PDB 3AVFb, dimer cavity

732598-732629

736025-736259

746578-746679

751219-751269

754669-754819

760932-760939

PDB 3AVGa, dimer cavity

732630-732661

736260-736494

746680-746781

751270-751320

754820-754970

760940-760947

PDB 3AVGb, dimer cavity

732662-732693

736495-736729

746782-746883

751321-751371

754971-755121

760948-760955

PDB 3AVHa, dimer cavity

732694-732725

736730-736964

746884-746985

751372-751422

755122-755272

760956-760963

PDB 3AVHb, dimer cavity

732726-732757

736965-737199

746986-747087

751423-751473

755273-755423

760964-760971

PDB 3AVIa, dimer cavity

732758-732789

737200-737434

747088-747189

751474-751524

755424-755574

760972-760979

PDB 3AVIb, dimer cavity

732790-732821

737435-737669

747190-747291

751525-751575

755575-755725

760980-760987

PDB 3AVJa, dimer cavity

732822-732853

737670-737904

747292-747393

751576-751626

755726-755876

760988-760995

PDB 3AVJb, dimer cavity

732854-732885

737905-738139

747394-747495

751627-751677

755877-756027

760996-761003

PDB 3AVKa, dimer cavity

732886-732917

738140-738374

747496-747597

751678-751728

756028-756178

761004-761011

PDB 3AVKb, dimer cavity

732918-732949

738375-738609

747598-747699

751729-751779

756179-756329

761012-761019

PDB 3AVLa, dimer cavity

732950-732981

738610-738844

747700-747801

751780-751830

756330-756480

761020-761027

PDB 3AVLb, dimer cavity

732982-733013

738845-739079

747802-747903

751831-751881

756481-756631

761028-761035

PDB 3AVMa, dimer cavity

733014-733045

739080-739314

747904-748005

751882-751932

756632-756782

761036-761043

PDB 3AVMb, dimer cavity

733046-733077

739315-739549

748006-748107

751933-751983

756783-756933

761044-761051

PDB 3AVNa, dimer cavity

733078-733109

739550-739784

748108-748209

751984-752034

756934-757084

761052-761059

PDB 3AVNb, dimer cavity

733110-733141

739785-740019

748210-748311

752035-752085

757085-757235

761060-761067

PDB 3NF6, dimer cavity

733142-733173

740020-740254

748312-748413

752086-752136

757236-757386

761068-761075

PDB 3NF7, dimer cavity

733174-733205

740255-740489

748414-748515

752137-752187

757387-757537

761076-761083

PDB 3NF8, dimer cavity

733206-733237

740490-740724

748516-748617

752188-752238

757538-757688

761084-761091

PDB 3NF9, dimer cavity

733238-733269

740725-740959

748618-748719

752239-752289

757689-757839

761092-761099

PDB 3NFA, dimer cavity

733270-733301

740960-741194

748720-748821

752290-752340

757840-757990

761100-761107

PDB 3VQ4, dimer cavity

733302-733333

741195-741429

748822-748923

752341-752391

757991-758141

761108-761115

PDB 3VQ5, dimer cavity

733334-733365

741430-741664

748924-749025

752392-752442

758142-758292

761116-761123

PDB 3VQ7, dimer cavity

733366-733397

741665-741899

749026-749127

752443-752493

758293-758443

761124-761131

PDB 3VQ8, dimer cavity

733398-733429

741900-742134

749128-749229

752494-752544

758444-758594

761132-761139

PDB 3VQA, dimer cavity

733430-733461

742135-742369

749230-749331

752545-752595

758595-758745

761140-761147

PDB 3VQD, dimer cavity

733462-733493

742370-742604

749332-749433

752596-752646

758746-758896

761148-761155

PDB 3VQE, dimer cavity

733494-733525

742605-742839

749434-749535

752647-752697

758897-759047

761156-761163

PDB 3ZCM, dimer cavity

733526-733557

742840-743074

749536-749637

752698-752748

759048-759198

761164-761171

PDB 3ZSO, dimer cavity

733558-733589

743075-743309

749638-749739

752749-752799

759199-759349

761172-761179

PDB 3ZSW, dimer cavity

733590-733621

743310-743544

749740-749841

752800-752850

759350-759500

761180-761187

PDB 3ZT1, dimer cavity

733622-733653

743545-743779

749842-749943

752851-752901

759501-759651

761188-761195

PDB 3ZT2, dimer cavity

733654-733685

743780-744014

749944-750045

752902-752952

759652-759802

761196-761203

PDB 3ZT3, dimer cavity

733686-733717

744015-744249

750046-750147

752953-753003

759803-759953

761204-761211

PDB 3ZT4, dimer cavity

733718-733749

744250-744484

750148-750249

753004-753054

759954-760104

761212-761219

PDB 4AHR, dimer cavity

733750-733781

744485-744719

750250-750351

753055-753105

760105-760255

761220-761227

PDB 4GVMa, dimer cavity

733782-733813

744720-744954

750352-750453

753106-753156

760256-760406

761228-761235

PDB 4GVMb, dimer cavity

733814-733845

744955-745189

750454-750555

753157-753207

760407-760557

761236-761243

PDB 4GW6a, dimer cavity

733846-733877

745190-745424

750556-750657

753208-753258

760558-760708

761244-761251

PDB 4GW6b, dimer cavity

733878-733909

745425-745659

750658-750759

753259-753309

760709-760859

761252-761259

COMPLETION

4%

95%

99.9%

74%

0%

0%

Experiments 127 to 132 (AD Vina), 23% completed

Experiments 127 through 132 target HIV reverse transcriptase. These experiments involve screening 6 libraries (Full NCI,
Enamine, ChemBridge, Asinex,
Vitas-M and Maybridge). These experiments will help determine the differences
and utility of varying the dimensions of a "docking box."

Experiments 121 through 126 target the active site of HIV protease. These experiments involve screening 6 libraries (Full NCI,
Enamine, ChemBridge, Asinex,
Vitas-M and Maybridge). These experiments will help determine the differences
and utility of varying the dimensions of a "docking box." The focus of these experiments is on the allosteric sites of HIV protease.

Results of these FightAIDS@Home experiments
are available to the public as raw, unprocessed AutoDock dlg files upon request.
E-mail Dr. Daniel N. Santiago = dsantiag ]~[ scripps . edu (use the @ symbol to replace the ]~[ and remove the spaces) for further information. Please
include the phrase "FAAH data" in the subject line of your e-mail.
Since the amount of data is on the order of many terabytes, you will need to provide
suitable media (such as external hard drives) for receiving a copy of these results.

Created by Dr. Garrett M. Morris and
curated by Dr. Alex L. Perryman from 2007 to August, 2013. Now curated by Dr. Daniel N. Santiago. The
HIVE logo above was created by Dr. Stefano Forli.
Last modified: 09/03/2014 by Daniel N. Santiago, Ph.D.